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Yuan T, Dong J, Jia B, Jiang H, Zhao Z, Zhou M. DTDHM: detection of tandem duplications based on hybrid methods using next-generation sequencing data. PeerJ 2024; 12:e17748. [PMID: 39076774 PMCID: PMC11285389 DOI: 10.7717/peerj.17748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/24/2024] [Indexed: 07/31/2024] Open
Abstract
Background Tandem duplication (TD) is a common and important type of structural variation in the human genome. TDs have been shown to play an essential role in many diseases, including cancer. However, it is difficult to accurately detect TDs due to the uneven distribution of reads and the inherent complexity of next-generation sequencing (NGS) data. Methods This article proposes a method called DTDHM (detection of tandem duplications based on hybrid methods), which utilizes NGS data to detect TDs in a single sample. DTDHM builds a pipeline that integrates read depth (RD), split read (SR), and paired-end mapping (PEM) signals. To solve the problem of uneven distribution of normal and abnormal samples, DTDHM uses the K-nearest neighbor (KNN) algorithm for multi-feature classification prediction. Then, the qualified split reads and discordant reads are extracted and analyzed to achieve accurate localization of variation sites. This article compares DTDHM with three other methods on 450 simulated datasets and five real datasets. Results In 450 simulated data samples, DTDHM consistently maintained the highest F1-score. The average F1-score of DTDHM, SVIM, TARDIS, and TIDDIT were 80.0%, 56.2%, 43.4%, and 67.1%, respectively. The F1-score of DTDHM had a small variation range and its detection effect was the most stable and 1.2 times that of the suboptimal method. Most of the boundary biases of DTDHM fluctuated around 20 bp, and its boundary deviation detection ability was better than TARDIS and TIDDIT. In real data experiments, five real sequencing samples (NA19238, NA19239, NA19240, HG00266, and NA12891) were used to test DTDHM. The results showed that DTDHM had the highest overlap density score (ODS) and F1-score of the four methods. Conclusions Compared with the other three methods, DTDHM achieved excellent results in terms of sensitivity, precision, F1-score, and boundary bias. These results indicate that DTDHM can be used as a reliable tool for detecting TDs from NGS data, especially in the case of low coverage depth and tumor purity samples.
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Affiliation(s)
- Tianting Yuan
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Jinxin Dong
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Baoxian Jia
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Hua Jiang
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Zuyao Zhao
- Orthopedics Department, Liaocheng People’s Hospital, Liaocheng, China
| | - Mengjiao Zhou
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
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2
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Martinez-Gutierrez LN, Burgher BC, Glynias MJ, Alvarado D, Griffiths EA, Glenn ST, Sung PJ. Evaluation of hypereosinophilia in a case of FLT3-mutant acute myeloid leukemia treated with gilteritinib. Cold Spring Harb Mol Case Stud 2023; 9:a006279. [PMID: 37433680 PMCID: PMC10393187 DOI: 10.1101/mcs.a006279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Acute myeloid leukemias (AMLs) frequently harbor activating mutations in Fms-like tyrosine kinase 3 (FLT3). The use of FLT3 inhibitors (FLT3i) is the standard of care for treatment of newly diagnosed and relapsed patients with AML. Differentiation responses including clinical differentiation syndrome have been previously reported with FLT3i when used as single agents in relapsed disease. We present a case of hypereosinophilia in a patient on FLT3i therapy with persistent FLT3 polymerase chain reaction (PCR) positivity in peripheral blood. We sorted mature leukocytes by lineage to determine if the eosinophils were leukemia-derived. FLT3 PCR and next-generation sequencing analysis demonstrated monocytic differentiation of the FLT3-ITD leukemic clone with reactive hypereosinophilia that was derived from a preleukemic SF3B1, FLT3 wild-type clone. Our case is the first to definitively demonstrate the emergence of clonal FLT3-ITD monocytes with FLT3i and the first to demonstrate a differentiation response following decitabine, venetoclax, and gilteritinib triplet therapy.
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Affiliation(s)
| | - Blake C Burgher
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Manuel J Glynias
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Daniel Alvarado
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Elizabeth A Griffiths
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Sean T Glenn
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Pamela J Sung
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA;
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
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3
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Lee JM, Park S, Hwang I, Kang D, Cho BS, Kim HJ, Ahn A, Kim M, Kim Y. FLT3-ITD Measurable Residual Disease Monitoring in Acute Myeloid Leukemia Using Next-Generation Sequencing. Cancers (Basel) 2022; 14:6121. [PMID: 36551616 PMCID: PMC9776673 DOI: 10.3390/cancers14246121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
The in-frame internal tandem duplication (ITD) of the FMS-like tyrosine kinase 3 (FLT3) gene is an important negative prognostic marker in acute myeloid leukemia (AML). FLT3-ITD monitoring is essential for patients at relapse or those receiving FLT3-targeted therapies. Fragment analysis (FA) is commonly used to detect and quantify FLT3-ITDs; however, detecting low-burden FLT3-ITDs after a treatment is challenging. We, therefore, developed a customized, next-generation sequencing (NGS)-based FLT3-ITD assay that includes a new ITD-tracing algorithm, "SEED", optimized for measurable residual disease (MRD) monitoring. NGS-SEED showed an enhanced sensitivity (0.001%) and has a superior performance over conventional fragment analysis. We further investigated the prognostic impact of MRD analyzed by NGS-SEED in AML patients who underwent allogeneic hematopoietic stem cell transplantation (HSCT). Our assay showed that the MRD assessed before and after HSCT were significantly associated with a risk of relapse and a poor overall survival, respectively, in a time-dependent analysis. Thus, this report highlighted the prognostic value of serial MRD monitoring using a sensitive method in a clinical setting of AML patients with FLT3-ITD.
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Affiliation(s)
- Jong-Mi Lee
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Silvia Park
- Department of Hematology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Leukemia Research Institute, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Insik Hwang
- Dow Biomedica Inc., Seoul 05771, Republic of Korea
| | - Dain Kang
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Byung Sik Cho
- Department of Hematology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Leukemia Research Institute, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Hee-Je Kim
- Department of Hematology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Leukemia Research Institute, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Ari Ahn
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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4
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Boudry A, Darmon S, Duployez N, Figeac M, Geffroy S, Bucci M, Celli-Lebras K, Duchmann M, Joudinaud R, Fenwarth L, Nibourel O, Goursaud L, Itzykson R, Dombret H, Hunault M, Preudhomme C, Salson M. Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r. BMC Bioinformatics 2022; 23:448. [PMID: 36307762 PMCID: PMC9617311 DOI: 10.1186/s12859-022-04983-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/07/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Internal tandem duplications in the FLT3 gene, termed FLT3-ITDs, are useful molecular markers in acute myeloid leukemia (AML) for patient risk stratification and follow-up. FLT3-ITDs are increasingly screened through high-throughput sequencing (HTS) raising the need for robust and efficient algorithms. We developed a new algorithm, which performs no alignment and uses little resources, to identify and quantify FLT3-ITDs in HTS data. RESULTS Our algorithm (FiLT3r) focuses on the k-mers from reads covering FLT3 exons 14 and 15. We show that those k-mers bring enough information to accurately detect, determine the length and quantify FLT3-ITD duplications. We compare the performances of FiLT3r to state-of-the-art alternatives and to fragment analysis, the gold standard method, on a cohort of 185 AML patients sequenced with capture-based HTS. On this dataset FiLT3r is more precise (no false positive nor false negative) than the other software evaluated. We also assess the software on public RNA-Seq data, which confirms the previous results and shows that FiLT3r requires little resources compared to other software. CONCLUSION FiLT3r is a free software available at https://gitlab.univ-lille.fr/filt3r/filt3r . The repository also contains a Snakefile to reproduce our experiments. We show that FiLT3r detects FLT3-ITDs better than other software while using less memory and time.
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Affiliation(s)
- Augustin Boudry
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Sasha Darmon
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000 Lille, France ,grid.15140.310000 0001 2175 9188ENS Lyon, Lyon, France
| | - Nicolas Duployez
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Martin Figeac
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, F-59000 Lille, France
| | - Sandrine Geffroy
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Maxime Bucci
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Karine Celli-Lebras
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Matthieu Duchmann
- grid.508487.60000 0004 7885 7602INSERM/CNRS UMR 944/7212, Saint-Louis Research Institute, Paris Diderot University, Paris, France
| | - Romane Joudinaud
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Laurène Fenwarth
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Olivier Nibourel
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Laure Goursaud
- grid.410463.40000 0004 0471 8845Hematology Department, CHU LILLE, Lille, France
| | - Raphael Itzykson
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France ,grid.508487.60000 0004 7885 7602INSERM/CNRS UMR 944/7212, Saint-Louis Research Institute, Paris Diderot University, Paris, France
| | - Hervé Dombret
- grid.413328.f0000 0001 2300 6614Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Mathilde Hunault
- grid.7252.20000 0001 2248 3363Univ Angers, Université de Nantes, CHU Angers, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000 Angers, France
| | - Claude Preudhomme
- grid.410463.40000 0004 0471 8845Hematology Laboratory, Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France ,grid.503422.20000 0001 2242 6780U1277 Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, INSERM, Lille, France
| | - Mikaël Salson
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000 Lille, France
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5
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Goh JY, Kuick CH, Sugiura M, Aw SJ, Zhao M, Tang H, Gunaratne S, Zhu F, Cai L, Teh BT, Thorner PS, Chang KTE. Paediatric
BCOR
‐associated sarcomas with a novel long spliced internal tandem duplication of
BCOR
exon 15. J Pathol Clin Res 2022; 8:470-480. [PMID: 35836306 PMCID: PMC9353662 DOI: 10.1002/cjp2.287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/14/2022] [Accepted: 06/22/2022] [Indexed: 11/08/2022]
Abstract
Clear cell sarcoma of the kidney (CCSK) and primitive myxoid mesenchymal tumour of infancy (PMMTI) are paediatric sarcomas that most commonly harbour internal tandem duplications (ITDs) of exon 15 of the BCOR gene, in the range of 87–114 base pairs (bp). Some cases, instead, have BCOR‐CCNB3 or YWHAE‐NUTM2 gene fusions. About 10% of cases lack any of these genetic alterations when tested by standard methods. Two cases of CCSK and one PMMTI lacking the aforementioned mutations were analysed using Archer FusionPlex technology. Two related BCOR exon 15 RNA transcripts with ITDs of lengths 388 and 96 bp were detected in each case; only the 388 bp transcript was identified when genomic DNA was sequenced. In silico analysis of this transcript revealed acceptor and donor splice sites indicating that, at the RNA level, the 388‐bp transcript was likely spliced to form the 96‐bp transcript. The results were confirmed by Sanger sequencing using primers targeting the ITD breakpoint. This novel and unusually long ITD segment is difficult to identify by DNA sequencing using typical primer design strategies flanking entire duplicated segments because it exceeds the typical read lengths of most sequencing platforms as well as the usual fragment lengths obtained from formalin‐fixed paraffin‐embedded material. As diagnosis of CCSK and PMMTI may be challenging by morphology and immunohistochemistry alone, it is important to identify mutations in these cases. Knowledge of this novel BCOR ITD is important in relation to primer design for detection by sequencing, and using RNA versus DNA for sequencing.
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Affiliation(s)
- Jian Yuan Goh
- Department of Pathology and Laboratory Medicine KK Women's and Children's Hospital Singapore
- Pathology Academic Clinical Programme SingHealth Duke‐NUS Medical School Singapore
| | - Chik Hong Kuick
- Department of Pathology and Laboratory Medicine KK Women's and Children's Hospital Singapore
| | - Masahiro Sugiura
- Department of Pathology and Laboratory Medicine KK Women's and Children's Hospital Singapore
| | - Sze Jet Aw
- Department of Pathology and Laboratory Medicine KK Women's and Children's Hospital Singapore
| | - Manli Zhao
- Department of Pathology The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health Hangzhou PR China
| | - Hongfeng Tang
- Department of Pathology The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health Hangzhou PR China
| | - Sandini Gunaratne
- Department of Pathology Lady Ridgeway Hospital for Children Colombo Sri Lanka
| | - Fucun Zhu
- Department of Pathology Fuzhou Children's Hospital of Fujian Province Fuzhou PR China
| | - Lin Cai
- Department of Pathology Fuzhou Children's Hospital of Fujian Province Fuzhou PR China
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome National Cancer Centre Singapore Singapore
- Cancer and Stem Cell Biology Programme Duke‐NUS Medical School Singapore
| | - Paul S Thorner
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
| | - Kenneth Tou En Chang
- Department of Pathology and Laboratory Medicine KK Women's and Children's Hospital Singapore
- Pathology Academic Clinical Programme SingHealth Duke‐NUS Medical School Singapore
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6
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FLT3 mutational analysis in acute myeloid leukemia: Advantages and pitfalls with different approaches. Blood Rev 2022; 54:100928. [DOI: 10.1016/j.blre.2022.100928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/17/2022]
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7
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Tung JK, Suarez CJ, Chiang T, Zehnder JL, Stehr H. Accurate Detection and Quantification of FLT3 Internal Tandem Duplications in Clinical Hybrid Capture Next-Generation Sequencing Data. J Mol Diagn 2021; 23:1404-1413. [PMID: 34363960 DOI: 10.1016/j.jmoldx.2021.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
FLT3 internal tandem duplications (ITDs) are found in approximately one-third of patients with acute myeloid leukemia and have important prognostic and therapeutic implications that have supported their assessment in routine clinical practice. Conventional methods for assessing FLT3-ITD status and allele burden have been primarily limited to PCR fragment size analysis because of the inherent difficulty in detecting large ITD variants by next-generation sequencing (NGS). In this study, we assess the performance of publicly available bioinformatic tools for the detection and quantification of FLT3-ITDs in clinical hybridization-capture NGS data. We found that FLT3_ITD_ext had the highest overall accuracy for detecting FLT3-ITDs and was able to accurately quantify allele burden. Although all other tools evaluated were able to detect FLT3-ITDs reasonably well, allele burden was consistently underestimated. We were able to significantly improve quantification of FLT3-ITD allelic burden independent of the detection method by utilizing soft-clipped reads and/or ITD junctional sequences. In addition, we show that identifying mutant reads by previously identified junctional sequences further improves the sensitivity of detecting FLT3-ITDs in post-treatment samples. Our results demonstrate that FLT3-ITDs can be reliably detected in clinical NGS data using available bioinformatic tools. We further describe how accurate quantification of FLT3-ITD allele burden can be added on to existing clinical NGS pipelines for routine assessment of FLT3-ITD status in patients with acute myeloid leukemia.
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Affiliation(s)
- Jack K Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Tsoyu Chiang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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8
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Yuan D, He X, Han X, Yang C, Liu F, Zhang S, Luan H, Li R, He J, Duan X, Wang D, Zhou Q, Gao S, Niu B. Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia. Brief Bioinform 2021; 22:6225087. [PMID: 33851200 DOI: 10.1093/bib/bbab099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/15/2021] [Accepted: 03/06/2021] [Indexed: 12/25/2022] Open
Abstract
Internal tandem duplication (ITD) of FMS-like tyrosine kinase 3 (FLT3-ITD) constitutes an independent indicator of poor prognosis in acute myeloid leukaemia (AML). AML with FLT3-ITD usually presents with poor treatment outcomes, high recurrence rate and short overall survival. Currently, polymerase chain reaction and capillary electrophoresis are widely adopted for the clinical detection of FLT3-ITD, whereas the length and mutation frequency of ITD are evaluated using fragment analysis. With the development of sequencing technology and the high incidence of FLT3-ITD mutations, a multitude of bioinformatics tools and pipelines have been developed to detect FLT3-ITD using next-generation sequencing data. However, systematic comparison and evaluation of the methods or software have not been performed. In this study, we provided a comprehensive review of the principles, functionality and limitations of the existing methods for detecting FLT3-ITD. We further compared the qualitative and quantitative detection capabilities of six representative tools using simulated and biological data. Our results will provide practical guidance for researchers and clinicians to select the appropriate FLT3-ITD detection tools and highlight the direction of future developments in this field. Availability: A Docker image with several programs pre-installed is available at https://github.com/niu-lab/docker-flt3-itd to facilitate the application of FLT3-ITD detection tools.
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Affiliation(s)
- Danyang Yuan
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in leukaemia-related bioinformatics and cancer genomics research. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu He
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in research related to the cancer genome and construction of the Chinese Cancer Genome Database. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Xinyin Han
- Computer Network Information Center, Chinese Academy of Sciences. He is mainly engaged in cancer genomics research focusing on the precise detection of tumour immunotherapy biomarkers. His affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Chunyan Yang
- Vice Director of the Laboratory of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in research regarding solid tumours and haematologic malignancy using multiple approaches, including next-generation sequencing. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Fei Liu
- bioinformatics analysis engineer of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in the collection of biological information and analysis of genomic and cancer data or other biological information. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Shuying Zhang
- Computer Network Information Center, Chinese Academy of Sciences. Her research mainly focuses on the cancer genome and bioinformatics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Haijing Luan
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in researching cancers of unknown primary sites (CUP) based on deep learning. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Ruilin Li
- Computer Network Information Center, Chinese Academy of Sciences. Her research interests include high-performance computing and bioinformatics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiayin He
- George Washington University. She is currently researching at the Computer Network Information Center, Chinese Academy of Sciences. Her research interests include biostatistics and computational statistics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaohong Duan
- Laboratory of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in the research of solid tumours and haematologic malignancies using multiple approaches, including next-generation sequencing. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Dongliang Wang
- Harbin Medical University. He is now the Chief Medical Officer of ChosenMed Technology (Beijing). His research mainly focuses on the mining and verification of molecular markers for tumour therapy. His affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Qiming Zhou
- CTO of ChosenMed Technology (Beijing) Co., Ltd. He is mainly engaged in the development of new molecular diagnostics technologies in genetic testing. His affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Sujun Gao
- Department of Haematology, The First Hospital of Jilin University. Her research mainly focuses on the experimental and clinical research of malignant haematological disorders and haematopoietic stem cell transplantation. Her affiliation is with Department of Haematology, The First Hospital of Jilin University, Changchun 130021, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences. His research interests include cancer genomics, metagenomics, and the development of computational tools for working with data from next-generation sequencing technologies. His affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China, ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
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9
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Wang TY, Yang R. ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation. Gigascience 2020; 9:giaa089. [PMID: 32852038 PMCID: PMC7450668 DOI: 10.1093/gigascience/giaa089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Internal tandem duplications (ITDs) are tandem duplications within coding exons and are important prognostic markers and drug targets for acute myeloid leukemia (AML). Next-generation sequencing has enabled the discovery of ITD at single-nucleotide resolution. ITD allele frequency is used in the risk stratification of patients with AML; higher ITD allele frequency is associated with poorer clinical outcomes. However, the ITD allele frequency data are often unavailable to treating physicians and the detection of ITDs with accurate variant allele frequency (VAF) estimation remains challenging for short-read sequencing. RESULTS Here we present the ScanITD approach, which performs a stepwise seed-and-realignment procedure for ITD detection with accurate VAF prediction. The evaluations on simulated and real data demonstrate that ScanITD outperforms 3 state-of-the-art ITD detectors, especially for VAF estimation. Importantly, ScanITD yields better accuracy than general-purpose structural variation callers for predicting ITD size range duplications. CONCLUSIONS ScanITD enables the accurate identification of ITDs with robust VAF estimation. ScanITD is written in Python and is open-source software that is freely accessible at https://github.com/ylab-hi/ScanITD.
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Affiliation(s)
- Ting-You Wang
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN 55912, USA
| | - Rendong Yang
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN 55912, USA
- Masonic Cancer Center, University of Minnesota, 425 E. River Pkwy, Minneapolis, MN 55455, USA
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